9CD2 | pdb_00009cd2

Structure of E. coli ZDHYS365 multi-ubiquitin domain protein

• PDB DOI: https://doi.org/10.2210/pdb9CD2/pdb

• Classification: PROTEIN BINDING
• Organism(s): Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-06-23 Released: 2025-04-02 
• Deposition Author(s): Ye, Q., Gong, M., Corbett, K.D.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.87 Å
• R-Value Free: 
  0.213 (Depositor), 0.212 (DCC) 
• R-Value Work: 
  0.182 (Depositor), 0.181 (DCC) 
• R-Value Observed: 
  0.183 (Depositor) 

Starting Model: in silico

Literature

Structural diversity and oligomerization of bacterial ubiquitin-like proteins.

Gong, M., Ye, Q., Gu, Y., Chambers, L.R., Bobkov, A.A., Arakawa, N.K., Matyszewski, M., Corbett, K.D.

(2025) Structure 33: 1016-1026.e4

• PubMed: 40250427 
• DOI: https://doi.org/10.1016/j.str.2025.03.011
• Primary Citation of Related Structures:  
  8U38, 9CD2, 9D59, 9D5A, 9D5B


• PubMed Abstract: 
  

  Bacteria possess a variety of operons with homology to eukaryotic ubiquitination pathways that encode predicted E1, E2, E3, deubiquitinase, and ubiquitin-like proteins. Some of these pathways have recently been shown to function in anti-bacteriophage immunity, but the biological functions of others remain unknown. Here, we show that ubiquitin-like proteins in two bacterial operon families show surprising architectural diversity, possessing one to three β-grasp domains preceded by diverse N-terminal domains. We find that a large group of bacterial ubiquitin-like proteins possess three β-grasp domains and form homodimers and helical filaments mediated by conserved Ca ²⁺ ion binding sites. Our findings highlight a distinctive mode of self-assembly for ubiquitin-like proteins and suggest that Ca ²⁺ -mediated ubiquitin-like protein filament assembly and/or disassembly enables cells to sense and respond to stress conditions that alter intracellular metal ion concentration.

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Organizational Affiliation: 
• Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA.
Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA.
Conrad Prebys Center for Chemical Genomics, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA.
Environmental and Complex Analysis Laboratory, Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA.
UC San Diego Cryo-EM Facility, University of California, San Diego, La Jolla, CA 92093, USA.
Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA; Department of Molecular Biology, University of California, San Diego, La Jolla, CA 92093, USA. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 51.51 kDa 
• Atom Count: 4,091 
• Modeled Residue Count: 436 
• Deposited Residue Count: 444 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ZDHYS365 multi-ubiquitin domain protein	A	222	Escherichia coli	Mutation(s): 0  Gene Names: GQE86_25035

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
ZDHYS365 multi-ubiquitin domain protein	B	222	Escherichia coli	Mutation(s): 0  Gene Names: GQE86_25035

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PG4	C [auth A], E [auth B]	TETRAETHYLENE GLYCOL C8 H18 O5 UWHCKJMYHZGTIT-UHFFFAOYSA-N
CA	D [auth A], F [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MLY	A	L-PEPTIDE LINKING	C8 H18 N2 O2		LYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.87 Å
• R-Value Free:  0.213 (Depositor), 0.212 (DCC) 
• R-Value Work:  0.182 (Depositor), 0.181 (DCC) 
• R-Value Observed: 0.183 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 117.538	α = 90
b = 117.538	β = 90
c = 104.444	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-04-02 
Deposition Author(s): Ye, Q., Gong, M., Corbett, K.D.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R35 GM144121

Revision History  

• Version 1.0: 2025-04-02
  Type: Initial release
  
• Version 1.1: 2025-10-15
  Changes: Database references